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| <pre> | | <pre> |
| Required General Parameters : | | Required General Parameters : |
− | --in <infile> : input BAM file name
| + | --in <infile> : input BAM file name |
− | --out <outfile> : output recalibration file name
| + | --out <outfile> : output recalibration file name |
− | Optional General Parameters : | + | Optional General Parameters : |
− | --log <logfile> : log and summary statistics (default: [outfile].log)
| + | --log <logfile> : log and summary statistics (default: [outfile].log) |
− | --verbose : Turn on verbose mode
| + | --verbose : Turn on verbose mode |
− | --noeof : do not expect an EOF block on a bam file.
| + | --noeof : do not expect an EOF block on a bam file. |
− | --params : print the parameter settings
| + | --params : print the parameter settings |
| | | |
| Recab Specific Required Parameters | | Recab Specific Required Parameters |
− | --refFile <reference file> : reference file name
| + | --refFile <reference file> : reference file name |
− | Recab Specific Optional Parameters : | + | Recab Specific Optional Parameters : |
− | --dbsnp <known variance file> : dbsnp file of positions
| + | --dbsnp <known variance file> : dbsnp file of positions |
− | --minBaseQual <minBaseQual> : minimum base quality of bases to recalibrate (default: 5)
| + | --minBaseQual <minBaseQual> : minimum base quality of bases to recalibrate (default: 5) |
− | --maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50)
| + | --maxBaseQual <maxBaseQual> : maximum recalibrated base quality (default: 50) |
− | --blended <weight> : blended model weight
| + | qualities over this value will be set to this value. |
− | --fitModel : check if the logistic regression model fits the data
| + | This setting is applied after binning (if applicable). |
− | overriden by fast, but automatically applied by useLogReg
| + | --blended <weight> : blended model weight |
− | --fast : use a compact representation that only allows:
| + | --fitModel : check if the logistic regression model fits the data |
− | * at most 256 Read Groups
| + | overriden by fast, but automatically applied by useLogReg |
− | * maximum quality 63
| + | --fast : use a compact representation that only allows: |
− | * at most 127 cycles
| + | * at most 256 Read Groups |
− | overrides fitModel, but is overridden by useLogReg
| + | * maximum quality 63 |
− | uses up to about 2.25G more memory than running without --fast.
| + | * at most 127 cycles |
− | --keepPrevDbsnp : do not exclude entries where the previous base is in dbsnp when
| + | overrides fitModel, but is overridden by useLogReg |
− | building the recalibration table
| + | uses up to about 2.25G more memory than running without --fast. |
− | By default they are excluded from the table.
| + | --keepPrevDbsnp : do not exclude entries where the previous base is in dbsnp when |
− | --keepPrevNonAdjacent : do not exclude entries where the previous base is not adjacent
| + | building the recalibration table |
− | (not a Cigar M/X/=) when building the recalibration table
| + | By default they are excluded from the table. |
− | By default they are excluded from the table (except the first cycle).
| + | --keepPrevNonAdjacent : do not exclude entries where the previous base is not adjacent |
− | --useLogReg : use logistic regression calculated quality for the new quality
| + | (not a Cigar M/X/=) when building the recalibration table |
− | automatically applies fitModel and overrides fast.
| + | By default they are excluded from the table (except the first cycle). |
− | --qualField <quality tag> : tag to get the starting base quality
| + | --useLogReg : use logistic regression calculated quality for the new quality |
− | (default is to get it from the Quality field)
| + | automatically applies fitModel and overrides fast. |
− | --storeQualTag <quality tag> : tag to store the previous quality into
| + | --qualField <quality tag> : tag to get the starting base quality |
− | --buildExcludeFlags <flag> : exclude reads with any of these flags set when building the
| + | (default is to get it from the Quality field) |
− | recalibration table
| + | --storeQualTag <quality tag> : tag to store the previous quality into |
− | --applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set
| + | --buildExcludeFlags <flag> : exclude reads with any of these flags set when building the |
| + | recalibration table. Default is 0xF04 |
| + | --applyExcludeFlags <flag> : do not apply the recalibration table to any reads with any of these flags set |
| + | Quality Binning Parameters (optional): |
| + | Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used) |
| + | Ranges are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70 |
| + | The first bin always starts at 0, so does not need to be specified. |
| + | By default, the bin value is the low end of the range. |
| + | --binQualS : Bin the Qualities as specified (phred): minQualOfBin2, minQualofBin3... |
| + | --binQualF : Bin the Qualities based on the specified file |
| + | --binMid : Use the mid point of the quality bin range for the quality value of the bin. |
| + | --binHigh : Use the high end of the quality bin range for the quality value of the bin. |
| + | |
| </pre> | | </pre> |
| {{PhoneHomeParamDesc}} | | {{PhoneHomeParamDesc}} |